@Sparkle No, but it is recommended that you have a few backups readily available just in case due to issues with older versions.
If you have some time please follow this guide to avoid losing work due to these potential issues.

If you’re just starting out with Pencil2D, the development team has been fixing a few bugs that have to do with saving and loading. Release version 0.6.2 and anove should minimize these issues download it here: http://pencil2d.org/download
However, In the event that you find yourself running upon those rare issues, please consider the following to prevent losing and, in some specific scenarios, also recover your work:
Always create backup copies of your work file BEFORE loading and AFTER sav…

@Sparkle It should not delete your progress as long as you save before closing the old version. Do not open both versions at the same time however, as that could cause issues to arise. Backups are also advised as @JoseMoreno mentioned.